Abstract
Systems biology requires comprehensive data at all molecular levels. Mass spectrometry (MS)-based proteomics has emerged as a powerful and universal method for the global measurement of proteins. In the most widespread format, it uses liquid chromatography (LC) coupled to high-resolution tandem mass spectrometry (MS/MS) to identify and quantify peptides at a large scale. This peptide intensity information is the basic quantitative proteomic data type. It is used to quantify proteins between different proteome states, including the temporal variation of the proteome, to determine the complete primary structure of proteins including posttranslational modifications, to localize proteins to organelles, and to determine protein interactions. Here, we describe the principles of analysis and the areas of biology where proteomics can make unique contributions. The large-scale nature of proteomics data and its high accuracy pose special opportunities as well as challenges in systems biology that have been largely untapped so far.
Keywords
ProteomicsProteomeComputational biologySystems biologyQuantitative proteomicsProteogenomicsMass spectrometryTandem mass spectrometryBottom-up proteomicsBiologyComputer scienceBioinformaticsChemistryProtein mass spectrometryGenomicsBiochemistryChromatographyGenome
Affiliated Institutions
Related Publications
Analysis of the Mouse Liver Proteome Using Advanced Mass Spectrometry
We report a large-scale analysis of mouse liver tissue comprising a novel fractionation approach and high-accuracy mass spectrometry techniques. Two fractions enriched for solub...
Analysis of Proteins and Proteomes by Mass Spectrometry
▪ Abstract A decade after the discovery of electrospray and matrix-assisted laser desorption ionization (MALDI), methods that finally allowed gentle ionization of large biomolec...
Rapid mass spectrometric peptide sequencing and mass matching for characterization of human melanoma proteins isolated by two-dimensional PAGE.
We report a general mass spectrometric approach for the rapid identification and characterization of proteins isolated by preparative two-dimensional polyacrylamide gel electrop...
Differential Analysis of Membrane Proteins in Mouse Fore- and Hindbrain Using a Label-Free Approach
The ability to quantitatively compare protein levels across different regions of the brain to identify disease mechanisms remains a fundamental research challenge. It requires b...
A Comparative Proteomic Study of Human Skin Suction Blister Fluid from Healthy Individuals Using Immunodepletion and iTRAQ Labeling
Aberrations in skin morphology and functionality can cause acute and chronic skin-related diseases that are the focus of dermatological research. Mechanically induced skin sucti...
Publication Info
- Year
- 2011
- Type
- review
- Volume
- 80
- Issue
- 1
- Pages
- 273-299
- Citations
- 673
- Access
- Closed
External Links
Social Impact
Altmetric
PlumX Metrics
Social media, news, blog, policy document mentions
Citation Metrics
673
OpenAlex
Cite This
Jürgen Cox,
Matthias Mann
(2011).
Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology.
Annual Review of Biochemistry
, 80
(1)
, 273-299.
https://doi.org/10.1146/annurev-biochem-061308-093216
Identifiers
- DOI
- 10.1146/annurev-biochem-061308-093216